BMRB Entry 19693

Name: Solution structure of oxidized dimeric form of human defensin 5
Published: 2014-09-08

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PDB ID: 2mit
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19693
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of oxidized dimeric form of human defensin 5

Deposition date:

2013-12-19

Original release date:

2014-09-08

Authors:

Ziarek, Joshua; Wommack, Andrew; Robson, Scott; Wagner, Gerhard; Nolan, Elizabeth

Citation:

Citation: Ziarek, Joshua; Wommack, Andrew; Robson, Scott; Wagner, Gerhard; Nolan, Elizabeth. "Discovery and Characterization of a Disulfide-Locked C2-Symmetric Defensin Peptide" J. Am. Chem. Soc. ., .-. (2014).
PubMed: 25181039

Assembly members:

Assembly members:
entity, polymer, 32 residues, 3594.227 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PJ201-TEV-HD5oxidized

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: ATCYCRTGRCATRESLSGVC EISGRLYRLCCR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	394
13C chemical shifts	236
15N chemical shifts	62

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	human_defensin_5 1	1
2	human_defensin_5 2	1

Entities:

Entity 1, human_defensin_5 1 32 residues - 3594.227 Da.

1

ALA

THR

CYS

TYR

CYS

ARG

THR

GLY

ARG

CYS

2

ALA

THR

ARG

GLU

SER

LEU

SER

GLY

VAL

CYS

3

GLU

ILE

SER

GLY

ARG

LEU

TYR

ARG

LEU

CYS

4

CYS

ARG

Samples:

sample_1: HD5, [U-99% 13C; U-99% 15N], 0.5 mM; H2O 90%; D2O 10%

sample_2: HD5, [U-99% 13C; U-99% 15N], 0.3 mM; HD5 0.3 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0 M; pH: 4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HNHB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift calculation, structure solution

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

WhatIF, Vriend - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Varian Avance 500 MHz

BMRB	18705
PDB	1ZMP 2LXZ 2MIT
EMBL	CCD28566
GB	AAA35754 AAH69690 AAI07080 AAT68886 ADQ32910
REF	NP_066290
SP	Q01523
AlphaFold	Q01523